Have a look at the ICAO Safety Management Manual (ICAO doc 9859), it gives a good overview of the basic tools used in aviation safety.
http://www.icao.int/fsix/_Library/SMM-9859_1ed_en.pdf
There are several methods, each has a particular usefulness to detect a certain type of information, some of the obvious ones:
- Air safety Reporting by frontline staff (WinBASIS or its successor Sentinel, are just databases which allow to store and analyse safety reports to detect safety trends, there are many others available), ASR systems provide sometimes high quality information on the why of some events, however the quantity is dependant on the willingness (and opportunities) of staff to report. It can be dodgy basing statistical analysis on ASR's.
- Flight data monitoring (provides a wealth of statistical data on a limited scope of in-flight parameters, which gives some info on how the aircraft is operated, but not why it is operated like that)
- Surveys (can give insight in attitudes of operators, but can't be treated as facts, more as an opinion poll)
- Line Operations Safety Audits (LOSA) (again a lot of statistical data on a limited field (TEM performance by pilots)
Each tool has its limitations, the more tools applied the more diverse viewpoints become available and a more complete image of the safety background becomes available. Keep in mind that all these hazard identification tools have their specific limitations!